Human Rights Watch (HRW) has accused the US government of covering up the extent of waterboarding at secret CIA prisons, alleging that Libyan opponents of Muammar Gaddafi were subjected to the torture before being handed over to the former dictator's security police.

The New York-based human rights group has cast "serious doubt" on Washington's claim that only three people, all members of al-Qaida, were waterboarded in American custody, claiming in a new report to have fresh evidence that the CIA used the technique to simulate drowning on Libyans snatched from countries in Africa and Asia.

The HRW report is based on documents seized at the Libyan intelligence headquarters after Gaddafi's fall, and interviews with 14 former detainees, mostly members of the Libyan Islamic Fighting Group (LIFG), which attempted for 20 years to overthrow the former regime in Tripoli. The group joined last year's revolution and some of those tortured by the US now hold leadership positions in the new Libyan administration.

Last week the US attorney general, Eric Holder, said that no one would be prosecuted for CIA abuses during the Bush administration's "war on terror" despite the death of at least two detainees under torture. But HRW said the latest revelations merit new independent inquiries in the US and Britain. It said Washington's failure to hold to account Americans responsible for torture undermines US demands for accountability for crimes by others in Syria and Libya.

Among those tortured was Khalid al-Sharif, who was held for two years in CIA-run detention centres in Afghanistan before being handed over to Gaddafi in 2005. He is now head of the Libyan National Guard.

"I spent three months getting interrogated heavily during the first period [in US custody] and they gave me a different type of torture every day. Sometimes they used water, sometimes not," he told HRW. "Sometimes they put a hood over my head and they lay me down and they started to put water in my mouth … They poured the water over my mouth and nose so I had the feeling that I was drowning. I couldn't breathe … I tried to turn my head left and right as much as I could to take in some gulps of breath. I felt as if I was suffocating."

Sharif told HRW a doctor was present who would tell the interrogators when to stop the abuse and when to continue.

"He said he felt like each time lasted about three minutes but said there was no way to really tell time," the HRW report states. "When told that the United States had admitted to doing this to a few people for between 20 and 40 seconds each time, he said he was sure his sessions were definitely longer than that.

"He said there were doctors present. He knows they were doctors because his leg was broken while he was there and he was treated by these same people. The doctors would monitor him as the cold water was poured on him, and when his body temperature got too low, they would order warm water be added to the cold. Once his temperature was okay, they would begin adding cold water again."

HRW said the testimony contradicts assertions in Washington about who was subject to the drowning technique, which the Bush administration claimed was not torture.

"The allegations cast serious doubts on prior assertions from US government officials that only three people were waterboarded in US custody," said HRW. "They also reflect just how little the public still knows about what went on in the US secret detention programme."

The report contains documents, some of which it said are being made public for the first time, found abandoned in the offices of former Libyan intelligence chief, Moussa Koussa, after Gaddafi was overthrown.

"The documents include communications between Moussa Koussa's office and the CIA, and between Koussa's office and MI6," the report said. "They show a high level of cooperation between the United States, the United Kingdom and the government of former Libyan leader Muammar Gaddafi on the transfer of Gaddafi's opponents into Libyan custody. The documents are significant because they shed light on the still opaque CIA renditions programme, identify former detainees by name, and provide corroborating evidence in several specific cases, most notably confirming the involvement of the US, the UK, and other governments.

"Ten of the 14 Libyans interviewed for this report were rendered back to Libya within about year of the date when Libya, the United States and the United Kingdom had formally mended their relations. The mending of relations was very publicly marked by a visit from the British prime minister at the time, Tony Blair, to Libya on 25 March, 2004. The collusion is ironic, given that years later these same governments would end up assisting Gaddafi's opponents in their efforts to overthrow the Libyan leader. Several of those opponents are now in leadership positions and are important political actors in Libya."

HRW said the treatment of the Libyans sheds light on the Bush administration's failure to distinguish between Islamists responsible for the 9/11 attacks and "those who may simply have been engaged in armed opposition against their own repressive regimes".

"This failure risked aligning the United States with brutal dictators and aided their efforts to dismiss all political opponents as terrorists," it said.